AN INTRODUCTION TO MOLECULAR PHYLOGENETIC ANALYSIS

Abstract

Phylogenetic analysis using molecular data such as DNA sequence for genes and amino acid sequence for proteins is very common not only in the field of evolutionary biology but also in the wide fields of molecular biology. The reason is that DNA sequencing became very popular and a huge amount of sequence data of genes and proteins are available in the public online database. Since many molecules (genes or proteins) which have various evolutionary rates are available, it is important to choose the suitable molecule for the phylogenetic analysis of a given lineage. For example, when the evolutionary rate of the gene (or protein) is too much higher for a given lineage, the substitution of nucleotide (or amino acid) is saturated. In this case, the accuracy of the phylogenetic analysis decreases. The methods for phylogenetic analysis are improving along with the evolution of computer science. Thus, there are many methods to infer phylogenetic tree, and many programs for each method are available. This mini review shows that general pattern of phylogenetic analysis, and explains some representative methods (Unweighted pair group method with arithmetic, Neighbor-joining method, Maximum parsimony method, maximum likelihood method, and Bayesian method). In the phylogenetic analysis, the most important feature is the interpretation of the phylogenetic tree. Therefore, several distinct points to evaluate a phylogenetic tree are also explained. These include, “validity of the tree shape”, “evolutionary distance”, and “validation of each internal branch”. Towards the end, the procedure of evaluating a phylogenetic tree with an example using MEGA 7 is presented.